Make sequence files recognized as a taxonomy

pkg/obiformats/taxonomy_read.go

@@ -0,0 +1,109 @@
+package obiformats
+
+import (
+	"fmt"
+	"os"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+	"github.com/gabriel-vasile/mimetype"
+
+	log "github.com/sirupsen/logrus"
+)
+
+type TaxonomyLoader func(path string, onlysn bool) (*obitax.Taxonomy, error)
+
+func DetectTaxonomyTarFormat(path string) (TaxonomyLoader, error) {
+
+	switch {
+	case IsNCBITarTaxDump(path):
+		log.Infof("NCBI Taxdump Tar Archive detected: %s", path)
+		return LoadNCBITarTaxDump, nil
+	}
+
+	return nil, fmt.Errorf("unknown taxonomy format: %s", path)
+}
+
+func DetectTaxonomyFormat(path string) (TaxonomyLoader, error) {
+
+	obiutils.RegisterOBIMimeType()
+
+	file, err := os.Open(path)
+	if err != nil {
+		return nil, err
+	}
+
+	fileInfo, err := file.Stat()
+	if err != nil {
+		file.Close()
+		return nil, err
+	}
+
+	file.Close()
+
+	if fileInfo.IsDir() {
+		// For the moment, we only support NCBI Taxdump directory format
+		log.Infof("NCBI Taxdump detected: %s", path)
+		return LoadNCBITaxDump, nil
+	} else {
+		file, err := obiutils.Ropen(path)
+
+		if err != nil {
+			return nil, err
+		}
+
+		mimetype, err := mimetype.DetectReader(file)
+
+		if err != nil {
+			file.Close()
+			return nil, err
+		}
+
+		file.Close()
+
+		switch mimetype.String() {
+		case "text/csv":
+			return LoadCSVTaxonomy, nil
+		case "application/x-tar":
+			return DetectTaxonomyTarFormat(path)
+		case "text/fasta":
+			return func(path string, onlysn bool) (*obitax.Taxonomy, error) {
+				input, err := ReadFastaFromFile(path)
+
+				if err != nil {
+					return nil, err
+				}
+				_, data := input.Load()
+
+				return data.ExtractTaxonomy(nil)
+			}, nil
+		case "text/fastq":
+			return func(path string, onlysn bool) (*obitax.Taxonomy, error) {
+				input, err := ReadFastqFromFile(path)
+
+				if err != nil {
+					return nil, err
+				}
+				_, data := input.Load()
+
+				return data.ExtractTaxonomy(nil)
+			}, nil
+		}
+
+		log.Fatalf("Detected file format: %s", mimetype.String())
+	}
+
+	return nil, nil
+}
+
+func LoadTaxonomy(path string, onlysn bool) (*obitax.Taxonomy, error) {
+	loader, err := DetectTaxonomyFormat(path)
+
+	if err != nil {
+		return nil, err
+	}
+
+	taxonomy, err := loader(path, onlysn)
+
+	return taxonomy, err
+}